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The discrete element method (DEM), based on JKR theory of adhesive elastic contacts, is used for three-dimensional simulations of micro-particle deposition and aggregation on an individual fiber of an array. An inlet–outlet boundary condition is introduced for the particles along the direction of flow and a periodic boundary condition is imposed in the other two directions. The DEM simulation predicts formation of dendrites which follow the three stages of dendrite formation—initial capture, fiber-dendrite capture, and complete dendrite capture—that have been identified in prior experimental studies. A dimensionless adhesion parameter is defined and shown to have a dominant effect on the predicted particle deposition rate. Particle capture is enhanced by decrease in either fluid viscosity or velocity, such that change in flow Reynolds number can have multiple effects depending on the variation of the other parameters.